DUF4416 - PFAM28P - GREMLIN Contacts

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DUF4416 - Domain of unknown function (DUF4416)

PFAM:	PF14385	Sequences: PVKLFVGVLSSDEEELLEEALERLEERFGPIDLESPPFPFDFTDYYEKEMGPPLKRRFLSFERLIDPEELADIKLATNELEEEFARDGKRRVNLDPGYLTLAKLVLATTKDYSHRIYLGDGIYAEVTLIYRKGSFQPLPWTYPDYRSPEYIEFFNRVREKY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	161 (160)
Sequences:	4820 (3824)
Seq/√Len:	302.3
META:	0.962

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_R	76_A	3.188	1.00
21_L	34_E	3.048	1.00
23_R	83_E	2.652	1.00
5_F	104_L	2.608	1.00
134_S	155_N	2.580	1.00
44_D	47_E	2.510	1.00
3_K	32_D	2.437	1.00
109_T	122_I	2.256	1.00
47_E	52_P	2.199	1.00
70_L	107_A	2.014	1.00
151_I	155_N	2.005	1.00
153_F	157_V	1.920	1.00
6_V	94_L	1.907	1.00
72_D	120_D	1.900	1.00
30_P	62_E	1.889	1.00
42_F	147_S	1.885	1.00
4_L	65_I	1.802	1.00
129_I	138_L	1.801	1.00
134_S	151_I	1.788	1.00
60_S	157_V	1.758	1.00
82_E	85_A	1.757	1.00
69_E	72_D	1.692	1.00
32_D	60_S	1.687	1.00
103_K	111_D	1.638	1.00
58_F	150_Y	1.576	1.00
100_T	103_K	1.568	1.00
65_I	73_I	1.546	1.00
33_L	153_F	1.540	1.00
39_P	55_K	1.530	1.00
12_D	15_E	1.522	1.00
34_E	57_R	1.510	1.00
8_V	94_L	1.496	1.00
2_V	67_P	1.494	1.00
148_P	152_E	1.492	1.00
4_L	28_F	1.487	1.00
9_L	56_R	1.475	1.00
76_A	79_E	1.473	1.00
9_L	54_L	1.447	1.00
4_L	73_I	1.440	1.00
102_A	111_D	1.415	1.00
72_D	119_G	1.404	1.00
65_I	98_Y	1.369	1.00
137_P	151_I	1.364	1.00
105_V	116_I	1.337	1.00
67_P	103_K	1.330	1.00
24_L	61_F	1.324	1.00
76_A	80_L	1.324	1.00
2_V	100_T	1.317	1.00
40_F	140_W	1.291	1.00
148_P	151_I	1.289	1.00
50_M	54_L	1.288	1.00
131_R	136_Q	1.274	1.00
118_L	124_A	1.265	1.00
37_P	57_R	1.242	1.00
8_V	59_L	1.239	1.00
104_L	154_F	1.225	1.00
6_V	24_L	1.207	1.00
28_F	73_I	1.193	1.00
78_N	122_I	1.188	1.00
100_T	111_D	1.181	1.00
6_V	61_F	1.178	1.00
7_G	56_R	1.172	1.00
23_R	84_F	1.153	1.00
113_S	129_I	1.144	1.00
71_A	119_G	1.142	1.00
116_I	124_A	1.138	1.00
156_R	159_E	1.122	1.00
131_R	139_P	1.120	1.00
47_E	54_L	1.117	1.00
25_E	30_P	1.115	1.00
20_A	84_F	1.102	1.00
10_S	37_P	1.088	1.00
102_A	112_Y	1.087	1.00
75_L	120_D	1.072	1.00
137_P	146_R	1.058	1.00
130_Y	135_F	1.051	1.00
147_S	150_Y	1.040	1.00
126_V	138_L	1.036	1.00
152_E	156_R	1.035	1.00
2_V	98_Y	1.031	1.00
99_L	104_L	1.026	1.00
23_R	26_E	1.023	1.00
86_R	91_R	1.017	1.00
65_I	69_E	1.014	1.00
115_R	125_E	1.007	1.00
25_E	31_I	0.996	1.00
112_Y	142_Y	0.991	1.00
56_R	144_D	0.987	1.00
111_D	123_Y	0.984	1.00
86_R	89_K	0.984	1.00
69_E	73_I	0.983	1.00
23_R	27_R	0.976	1.00
38_F	56_R	0.973	1.00
68_E	119_G	0.971	1.00
28_F	76_A	0.969	1.00
21_L	25_E	0.968	1.00
106_L	127_T	0.965	1.00
3_K	60_S	0.958	1.00
67_P	100_T	0.957	1.00
22_E	25_E	0.954	1.00
33_L	157_V	0.953	1.00
7_G	58_F	0.949	1.00
135_F	155_N	0.949	1.00
5_F	60_S	0.947	1.00
71_A	120_D	0.947	1.00
21_L	59_L	0.946	1.00
47_E	53_P	0.942	1.00
22_E	26_E	0.933	1.00
103_K	116_I	0.931	1.00
5_F	157_V	0.927	1.00
111_D	116_I	0.926	1.00
79_E	82_E	0.922	1.00
67_P	102_A	0.916	1.00
150_Y	154_F	0.913	1.00
40_F	43_T	0.902	1.00
129_I	139_P	0.891	1.00
78_N	109_T	0.886	1.00
64_L	161_Y	0.886	1.00
60_S	153_F	0.880	1.00
33_L	156_R	0.869	1.00
10_S	16_L	0.863	1.00
18_E	22_E	0.855	1.00
14_E	18_E	0.854	1.00
12_D	91_R	0.853	1.00
102_A	113_S	0.851	1.00
19_E	22_E	0.849	1.00
14_E	37_P	0.847	1.00
115_R	142_Y	0.844	1.00
10_S	17_L	0.834	1.00
20_A	92_V	0.819	1.00
108_T	142_Y	0.818	1.00
58_F	154_F	0.816	1.00
75_L	78_N	0.815	1.00
8_V	17_L	0.808	1.00
49_E	91_R	0.807	1.00
79_E	83_E	0.804	1.00
136_Q	139_P	0.800	1.00
32_D	160_K	0.796	1.00
15_E	18_E	0.793	1.00
103_K	129_I	0.792	1.00
9_L	50_M	0.785	0.99
75_L	122_I	0.783	0.99
16_L	91_R	0.781	0.99
73_I	96_P	0.779	0.99
135_F	151_I	0.777	0.99
14_E	55_K	0.777	0.99
19_E	23_R	0.771	0.99
68_E	117_Y	0.765	0.99
3_K	157_V	0.763	0.99
132_K	136_Q	0.758	0.99
31_I	34_E	0.756	0.99
118_L	122_I	0.749	0.99
113_S	138_L	0.748	0.99
98_Y	105_V	0.744	0.99
35_S	38_F	0.736	0.99
72_D	76_A	0.735	0.99
11_S	54_L	0.722	0.99
34_E	59_L	0.720	0.99
98_Y	103_K	0.718	0.99
38_F	153_F	0.718	0.99
112_Y	115_R	0.716	0.99
33_L	60_S	0.711	0.99
73_I	77_T	0.711	0.99
115_R	145_Y	0.709	0.99
16_L	19_E	0.699	0.99
84_F	91_R	0.698	0.99
6_V	77_T	0.696	0.99
124_A	127_T	0.695	0.99
115_R	127_T	0.687	0.99
31_I	61_F	0.685	0.99
10_S	20_A	0.682	0.99
108_T	112_Y	0.679	0.98
71_A	75_L	0.673	0.98
8_V	92_V	0.670	0.98
38_F	58_F	0.668	0.98
17_L	57_R	0.667	0.98
85_A	89_K	0.662	0.98
21_L	57_R	0.659	0.98
37_P	55_K	0.658	0.98
71_A	107_A	0.658	0.98
6_V	59_L	0.655	0.98
68_E	71_A	0.654	0.98
67_P	123_Y	0.653	0.98
106_L	125_E	0.652	0.98
129_I	136_Q	0.644	0.98
84_F	92_V	0.642	0.98
108_T	114_H	0.634	0.98
85_A	91_R	0.631	0.98
108_T	113_S	0.629	0.98
11_S	91_R	0.628	0.98
42_F	145_Y	0.626	0.97
109_T	125_E	0.623	0.97
67_P	117_Y	0.623	0.97
113_S	131_R	0.614	0.97
125_E	142_Y	0.608	0.97
143_P	146_R	0.606	0.97
24_L	80_L	0.600	0.97
80_L	84_F	0.594	0.97
36_P	149_E	0.593	0.96
78_N	82_E	0.585	0.96
109_T	115_R	0.584	0.96
108_T	125_E	0.582	0.96
33_L	160_K	0.581	0.96
105_V	124_A	0.567	0.95
12_D	16_L	0.566	0.95
78_N	107_A	0.561	0.95
16_L	20_A	0.556	0.95
48_K	89_K	0.556	0.95
75_L	79_E	0.556	0.95
10_S	14_E	0.554	0.95
46_Y	110_K	0.554	0.95
117_Y	125_E	0.553	0.95
45_Y	110_K	0.550	0.95
39_P	53_P	0.548	0.95
139_P	146_R	0.547	0.95
2_V	117_Y	0.547	0.95
140_W	144_D	0.547	0.95
126_V	140_W	0.545	0.94
114_H	126_V	0.541	0.94
100_T	112_Y	0.540	0.94
8_V	57_R	0.539	0.94
35_S	57_R	0.538	0.94
62_E	160_K	0.533	0.94
78_N	121_G	0.530	0.94
106_L	145_Y	0.525	0.93
118_L	121_G	0.525	0.93
44_D	52_P	0.523	0.93
15_E	19_E	0.521	0.93
90_R	93_N	0.521	0.93
152_E	155_N	0.520	0.93
71_A	118_L	0.519	0.93
138_L	141_T	0.519	0.93
41_D	149_E	0.518	0.93
63_R	69_E	0.518	0.93
10_S	57_R	0.509	0.92
3_K	160_K	0.508	0.92
1_P	66_D	0.508	0.92
101_L	113_S	0.507	0.92
104_L	135_F	0.501	0.92
109_T	127_T	0.500	0.91

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2q0oA	2	0.6522	8.8	0.957	Contact Map
3d45A	2	0.5528	8.3	0.957	Contact Map
3biyA	1	0.8385	7.7	0.958	Contact Map
3wvzA	2	0.528	6.2	0.96	Contact Map
1vcoA	4	0.6211	5.4	0.961	Contact Map
2id1A	1	0.5714	5.4	0.961	Contact Map
4zdjA	4	0.6273	5.3	0.961	Contact Map
2o5aA	2	0.559	5.2	0.961	Contact Map
4bhwA	2	0.8385	4.9	0.961	Contact Map
4wcwA	2	0.5901	4.8	0.962	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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